pacman::p_load("cowplot","dismo","leaflet","maps","mapdata","OpenStreetMap","raster","rasterVis","readxl","rgbif","rgdal","tidyverse","utils", "rvertnet", "rinat")
## Installing package into 'C:/Users/Conno/OneDrive/Documents/R/win-library/4.1'
## (as 'lib' is unspecified)
## Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/4.1:
## cannot open URL 'http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/4.1/PACKAGES'
## package 'OpenStreetMap' successfully unpacked and MD5 sums checked
##
## The downloaded binary packages are in
## C:\Users\Conno\AppData\Local\Temp\Rtmp2HlKK9\downloaded_packages
##
## OpenStreetMap installed
## Warning in pacman::p_load("cowplot", "dismo", "leaflet", "maps", "mapdata", : Failed to install/load:
## OpenStreetMap
library(mgsub)
library(lubridate)
##
## Attaching package: 'lubridate'
## The following objects are masked from 'package:raster':
##
## intersect, union
## The following object is masked from 'package:cowplot':
##
## stamp
## The following objects are masked from 'package:base':
##
## date, intersect, setdiff, union
state <- map_data("state")
county <- map_data("county")
tn <- county %>%
filter(region=="tennessee")
x <- tn[1]
y <- tn[2]
tn_SP <- FRK::df_to_SpatialPolygons(tn, "subregion", c("long", "lat"), proj = CRS("+init=epsg:4269"))
tn_SP <- spTransform(tn_SP, "+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs")
APSU_Marbled <- read.csv("https://raw.githubusercontent.com/CJHughes926/Herpmapping_Map_Assignment2/main/APSU_Ambystoma_opacum_TN.csv")
Vertnet_Marbled <- rvertnet::searchbyterm(scientificname = "Ambystoma opacum", stateprovince = "Tennessee", limit = 10000)
## Processing request...
##
## Last Query URL: "http://api.vertnet-portal.appspot.com/api/search?q={"q":"scientificname:Ambystoma opacum stateprovince:Tennessee","l":10000}"
##
## Matching records: 117 returned, 117 available
Vertnet_Marbled <- Vertnet_Marbled$data
Inat_Marbled <- rinat::get_inat_obs(taxon_name = "Ambystoma opacum", place_id = 45, maxresults = 1000, quality = "research", geo = TRUE)
GBif_Marbled <- rgbif::occ_data(scientificName = "Ambystoma opacum",
hasCoordinate = TRUE, limit = 5000,
decimalLongitude = "-91, -81",
decimalLatitude = "34, 37", )
GBif_Marbled <- GBif_Marbled$data
APSU_Marbled <- as.data.frame(APSU_Marbled)
APSU_Marbled <- subset(APSU_Marbled, is.na(APSU_Marbled$DEC_LAT) == FALSE)
APSU_Marbled <- subset(APSU_Marbled, APSU_Marbled$STATE_PROV == "Tennessee")
APSU_Marbled$COUNTY <- mgsub(APSU_Marbled$COUNTY, " County", "")
Vertnet_Marbled <- as.data.frame(Vertnet_Marbled)
Vertnet_Marbled <- subset(Vertnet_Marbled, is.na(Vertnet_Marbled$decimallatitude) == FALSE)
Vertnet_Marbled <- subset(Vertnet_Marbled, is.na(Vertnet_Marbled$decimallongitude) == FALSE)
Vertnet_Marbled$county <- mgsub(Vertnet_Marbled$county, " County", "")
Vertnet_Marbled$decimallatitude <- as.numeric(Vertnet_Marbled$decimallatitude)
Vertnet_Marbled$decimallongitude <- as.numeric(Vertnet_Marbled$decimallongitude)
Inat_Marbled <- as.data.frame(Inat_Marbled, )
Inat_Marbled <- subset(Inat_Marbled, Inat_Marbled$coordinates_obscured == "false")
Inat_Marbled <- subset(Inat_Marbled, is.na(Inat_Marbled$latitude) == FALSE)
GBif_Marbled <- as.data.frame(GBif_Marbled)
GBif_Marbled <- subset(GBif_Marbled, is.na(GBif_Marbled$decimalLatitude) == FALSE)
GBif_Marbled <- subset(GBif_Marbled, GBif_Marbled$stateProvince == "tennessee" | GBif_Marbled$stateProvince == "Tennessee" | GBif_Marbled$stateProvince == "TN" | GBif_Marbled$stateProvince == "tn")
County_Counts <- as.data.frame(toupper(unique(tn$subregion)))
names(County_Counts)[1] <- "County"
Vertnet_Counts <- mutate(as.data.frame(table(Vertnet_Marbled$county)))
APSU_Counts <- mutate(as.data.frame(table(APSU_Marbled$COUNTY)))
Vertnet_Counts$Var1 <- toupper(Vertnet_Counts$Var1)
names(Vertnet_Counts)[1] <- "County"
APSU_Counts$Var1 <- toupper(APSU_Counts$Var1)
names(APSU_Counts)[1] <- "County"
County_Counts$Total <- 0
County_Counts <- merge(County_Counts, APSU_Counts, all.x = TRUE)
names(County_Counts)[names(County_Counts) == 'Freq'] <- "Vertnet_Counts"
County_Counts <- merge(County_Counts, Vertnet_Counts, all.x = TRUE)
names(County_Counts)[names(County_Counts) == 'Freq'] <- "APSU_Counts"
County_Counts <- County_Counts %>% replace_na(list(Vertnet_Counts = 0, APSU_Counts = 0))
County_Counts$Total <- County_Counts$Vertnet_Counts + County_Counts$APSU_Counts
County_Counts
## County Total Vertnet_Counts APSU_Counts
## 1 ANDERSON 0 0 0
## 2 BEDFORD 0 0 0
## 3 BENTON 1 0 1
## 4 BLEDSOE 0 0 0
## 5 BLOUNT 7 0 7
## 6 BRADLEY 1 0 1
## 7 CAMPBELL 0 0 0
## 8 CANNON 0 0 0
## 9 CARROLL 0 0 0
## 10 CARTER 0 0 0
## 11 CHEATHAM 3 3 0
## 12 CHESTER 0 0 0
## 13 CLAIBORNE 1 0 1
## 14 CLAY 0 0 0
## 15 COCKE 0 0 0
## 16 COFFEE 0 0 0
## 17 CROCKETT 0 0 0
## 18 CUMBERLAND 0 0 0
## 19 DAVIDSON 0 0 0
## 20 DE KALB 0 0 0
## 21 DECATUR 3 0 3
## 22 DICKSON 3 3 0
## 23 DYER 6 0 6
## 24 FAYETTE 3 1 2
## 25 FENTRESS 0 0 0
## 26 FRANKLIN 2 2 0
## 27 GIBSON 1 0 1
## 28 GILES 0 0 0
## 29 GRAINGER 0 0 0
## 30 GREENE 0 0 0
## 31 GRUNDY 0 0 0
## 32 HAMBLEN 0 0 0
## 33 HAMILTON 0 0 0
## 34 HANCOCK 0 0 0
## 35 HARDEMAN 0 0 0
## 36 HARDIN 1 0 1
## 37 HAWKINS 1 1 0
## 38 HAYWOOD 0 0 0
## 39 HENDERSON 1 1 0
## 40 HENRY 0 0 0
## 41 HICKMAN 0 0 0
## 42 HOUSTON 1 1 0
## 43 HUMPHREYS 0 0 0
## 44 JACKSON 0 0 0
## 45 JEFFERSON 0 0 0
## 46 JOHNSON 0 0 0
## 47 KNOX 0 0 0
## 48 LAKE 1 0 1
## 49 LAUDERDALE 0 0 0
## 50 LAWRENCE 1 1 0
## 51 LEWIS 1 1 0
## 52 LINCOLN 2 1 1
## 53 LOUDON 0 0 0
## 54 MACON 0 0 0
## 55 MADISON 0 0 0
## 56 MARION 3 3 0
## 57 MARSHALL 0 0 0
## 58 MAURY 0 0 0
## 59 MCMINN 0 0 0
## 60 MCNAIRY 0 0 0
## 61 MEIGS 0 0 0
## 62 MONROE 0 0 0
## 63 MONTGOMERY 13 13 0
## 64 MOORE 0 0 0
## 65 MORGAN 0 0 0
## 66 OBION 5 0 5
## 67 OVERTON 0 0 0
## 68 PERRY 0 0 0
## 69 PICKETT 0 0 0
## 70 POLK 0 0 0
## 71 PUTNAM 5 0 5
## 72 RHEA 0 0 0
## 73 ROANE 0 0 0
## 74 ROBERTSON 1 1 0
## 75 RUTHERFORD 0 0 0
## 76 SCOTT 0 0 0
## 77 SEQUATCHIE 0 0 0
## 78 SEVIER 0 0 0
## 79 SHELBY 2 0 2
## 80 SMITH 0 0 0
## 81 STEWART 32 32 0
## 82 SULLIVAN 1 1 0
## 83 SUMNER 1 0 1
## 84 TIPTON 0 0 0
## 85 TROUSDALE 0 0 0
## 86 UNICOI 0 0 0
## 87 UNION 1 1 0
## 88 VAN BUREN 0 0 0
## 89 WARREN 0 0 0
## 90 WASHINGTON 0 0 0
## 91 WAYNE 0 0 0
## 92 WEAKLEY 1 0 1
## 93 WHITE 0 0 0
## 94 WILLIAMSON 1 1 0
## 95 WILSON 0 0 0
totalsamples = list()
for (county in subset(County_Counts$County, County_Counts$Total > 0)) {
print(county)
cty <- subset(tn, subregion==tolower(county))
x <- cty[1]
y <- cty[2]
points <- subset(County_Counts$Total, County_Counts$County == toupper(county))
ctypoly1 <- sp::Polygon(cbind(x,y))
ctypoly1 <- sp::Polygons(list(ctypoly1), ID = "A")
samples <- spsample(ctypoly1,n=points,"random")
samples <- as.data.frame(samples@coords)
totalsamples[[county]] <- samples }
## [1] "BENTON"
## [1] "BLOUNT"
## [1] "BRADLEY"
## [1] "CHEATHAM"
## [1] "CLAIBORNE"
## [1] "DECATUR"
## [1] "DICKSON"
## [1] "DYER"
## [1] "FAYETTE"
## [1] "FRANKLIN"
## [1] "GIBSON"
## [1] "HARDIN"
## [1] "HAWKINS"
## [1] "HENDERSON"
## [1] "HOUSTON"
## [1] "LAKE"
## [1] "LAWRENCE"
## [1] "LEWIS"
## [1] "LINCOLN"
## [1] "MARION"
## [1] "MONTGOMERY"
## [1] "OBION"
## [1] "PUTNAM"
## [1] "ROBERTSON"
## [1] "SHELBY"
## [1] "STEWART"
## [1] "SULLIVAN"
## [1] "SUMNER"
## [1] "UNION"
## [1] "WEAKLEY"
## [1] "WILLIAMSON"
Obscured_Records = as.data.frame(do.call(rbind, totalsamples))
Obscured_Records = Obscured_Records[1:2]
Vertnet_Marbled$GUID <- paste(Vertnet_Marbled$institutioncode,":", Vertnet_Marbled$catalognumber, sep = "")
Specimen_List1 <- Vertnet_Marbled %>% group_by(county) %>%
summarize(Specimen1 = paste(sort(unique(GUID)),collapse=", "))
names(Specimen_List1)[names(Specimen_List1) == 'county'] <- "COUNTY"
Specimen_List1$COUNTY <- toupper(Specimen_List1$COUNTY)
Specimen_List2 <- APSU_Marbled %>% group_by(COUNTY) %>%
summarize(Specimen2 = paste(sort(unique(GUID)),collapse=", "))
Specimen_List2$COUNTY <- toupper(Specimen_List2$COUNTY)
Specimen_List <- merge(Specimen_List1, Specimen_List2, all = TRUE, by = "COUNTY")
Specimen_List$Specimens <- paste(Specimen_List$Specimen1, Specimen_List$Specimen2, sep = ", ")
Specimen_List$Specimen1 <- NULL
Specimen_List$Specimen2 <- NULL
Specimen_List$Specimens <- mgsub(Specimen_List$Specimens, "NA", "")
substr(Specimen_List$Specimens, 1, 2)
## [1] "US" "MV" "NC" ", " "YP" "KU" ", " "US" "US" ", " "YP" "UF" ", " ", " ", "
## [16] "CU" ", " ", " "UF" ", " ", " "KU" "NC" ", " "NC" ", " ", " "US" ", " "KU"
## [31] ", "
Specimen_List
## COUNTY
## 1 BENTON
## 2 BLOUNT
## 3 BRADLEY
## 4 CHEATHAM
## 5 CLAIBORNE
## 6 DECATUR
## 7 DICKSON
## 8 DYER
## 9 FAYETTE
## 10 FRANKLIN
## 11 GIBSON
## 12 HARDIN
## 13 HAWKINS
## 14 HENDERSON
## 15 HOUSTON
## 16 LAKE
## 17 LAWRENCE
## 18 LEWIS
## 19 LINCOLN
## 20 MARION
## 21 MONTGOMERY
## 22 OBION
## 23 PUTNAM
## 24 ROBERTSON
## 25 SHELBY
## 26 STEWART
## 27 SULLIVAN
## 28 SUMNER
## 29 UNION
## 30 WEAKLEY
## 31 WILLIAMSON
## Specimens
## 1 USNM:45958,
## 2 MVZ:MVZ:Herp:40946, USNM:540940, USNM:540941, USNM:540942, USNM:540943, USNM:540944, USNM:540945,
## 3 NCSM:61623,
## 4 , APSU:Herp:03532, APSU:Herp:04007, APSU:Herp:19270
## 5 YPM:YPM HERA 013670,
## 6 KU:2639, KU:2640, KU:2641,
## 7 , APSU:Herp:02776, APSU:Herp:03159, APSU:Herp:20066
## 8 USNM:28394, USNM:28395, USNM:28396, USNM:28397, USNM:28398, USNM:28399,
## 9 USNM:99130, USNM:99131, APSU:Herp:18050
## 10 , APSU:Herp:03257, APSU:Herp:06024
## 11 YPM:YPM HERA 020516,
## 12 UF:171994,
## 13 , APSU:Herp:18168
## 14 , APSU:Herp:19197
## 15 , APSU:Herp:06056
## 16 CUMV:A-0003507,
## 17 , APSU:Herp:17622
## 18 , APSU:Herp:17623
## 19 UF:171982, APSU:Herp:19974
## 20 , APSU:Herp:17627, APSU:Herp:17628, APSU:Herp:17644
## 21 , APSU:Herp:02044, APSU:Herp:03026, APSU:Herp:03311, APSU:Herp:04293, APSU:Herp:05199, APSU:Herp:05200, APSU:Herp:05210, APSU:Herp:05305, APSU:Herp:05313, APSU:Herp:05316, APSU:Herp:05356, APSU:Herp:05362, APSU:Herp:05400
## 22 KU:155854, KU:155855, KU:155856, KU:155857, USNM:103100,
## 23 NCSM:8683, NCSM:8684, NCSM:8685, NCSM:8686, NCSM:8687,
## 24 , APSU:Herp:02925
## 25 NCSM:235, USNM:6449,
## 26 , APSU:Herp:00920, APSU:Herp:02801, APSU:Herp:03758, APSU:Herp:04655, APSU:Herp:04895, APSU:Herp:04984, APSU:Herp:04985, APSU:Herp:05005, APSU:Herp:05043, APSU:Herp:05051, APSU:Herp:05057, APSU:Herp:05062, APSU:Herp:05211, APSU:Herp:05388, APSU:Herp:05417, APSU:Herp:05513, APSU:Herp:05519, APSU:Herp:05528, APSU:Herp:05668, APSU:Herp:05697, APSU:Herp:05732, APSU:Herp:05735, APSU:Herp:05736, APSU:Herp:05749, APSU:Herp:05806, APSU:Herp:05807, APSU:Herp:05893, APSU:Herp:05894, APSU:Herp:05902, APSU:Herp:05997, APSU:Herp:05998, APSU:Herp:18045
## 27 , APSU:Herp:18170
## 28 USNM:3933,
## 29 , APSU:Herp:17709
## 30 KU:98590,
## 31 , APSU:Herp:19656
ggplot() +
geom_polygon(data = state, aes(x=long, y = lat, group = group),
fill = "white", color="black") +
geom_polygon(data = tn, aes(x=long, y = lat, group = group),
fill = "gray", color="black") +
geom_point(data = Obscured_Records, aes(x = Obscured_Records$x, y = Obscured_Records$y), color = "black", size = 2) +
coord_fixed(xlim = c(-90.5, -81.5), ylim = c(34.75, 36.75), ratio = 1.2) +
xlab("Longitude") + ylab("Latitude") + ggtitle("APSU, Montgomery Co., TN")
## Warning: Use of `Obscured_Records$x` is discouraged. Use `x` instead.
## Warning: Use of `Obscured_Records$y` is discouraged. Use `y` instead.
ggplot() +
geom_polygon(data = state, aes(x=long, y = lat, group = group),
fill = "white", color="black") +
geom_polygon(data = tn, aes(x=long, y = lat, group = group),
fill = "gray", color="black") +
geom_point(data = Inat_Marbled, aes(Inat_Marbled$longitude, Inat_Marbled$latitude), color = "#1f7d1f", size = 2) +
geom_point(data = GBif_Marbled, aes(GBif_Marbled$decimalLongitude, GBif_Marbled$decimalLatitude), color = "dark blue", size = 2) +
geom_point(data = Vertnet_Marbled, aes(Vertnet_Marbled$decimallongitude, Vertnet_Marbled$decimallatitude), color = "dark orange", size = 2) +
geom_point(data = APSU_Marbled, aes(x = APSU_Marbled$DEC_LONG, y = APSU_Marbled$DEC_LAT), color = "maroon", size = 2) +
coord_fixed(xlim = c(-90.5, -81.5), ylim = c(34.75, 36.75), ratio = 1.2) +
xlab("Longitude") + ylab("Latitude") + ggtitle("APSU, Montgomery Co., TN")
## Warning: Use of `Inat_Marbled$longitude` is discouraged. Use `longitude`
## instead.
## Warning: Use of `Inat_Marbled$latitude` is discouraged. Use `latitude` instead.
## Warning: Use of `GBif_Marbled$decimalLongitude` is discouraged. Use
## `decimalLongitude` instead.
## Warning: Use of `GBif_Marbled$decimalLatitude` is discouraged. Use
## `decimalLatitude` instead.
## Warning: Use of `Vertnet_Marbled$decimallongitude` is discouraged. Use
## `decimallongitude` instead.
## Warning: Use of `Vertnet_Marbled$decimallatitude` is discouraged. Use
## `decimallatitude` instead.
## Warning: Use of `APSU_Marbled$DEC_LONG` is discouraged. Use `DEC_LONG` instead.
## Warning: Use of `APSU_Marbled$DEC_LAT` is discouraged. Use `DEC_LAT` instead.
label <- toupper(c(County_Counts$County))
leaflet(APSU_Marbled) %>%
addTiles(group = "Base Map") %>%
addWMSTiles("https://basemap.nationalmap.gov/arcgis/services/USGSTopo/MapServer/WmsServer", layers = "0", group = "Terrain Map") %>%
addPolygons(data= tn_SP, fillColor = "white", color = "black", weight = 1, label = label) %>%
addCircleMarkers(data = Vertnet_Marbled, lng=Vertnet_Marbled$decimallongitude, lat=Vertnet_Marbled$decimallatitude, color = "orange", radius = .5, label = as.Date(Vertnet_Marbled$eventdate), group = "Vertnet Records") %>%
addCircleMarkers(data = GBif_Marbled, lng=GBif_Marbled$decimalLongitude, lat=GBif_Marbled$decimalLatitude, color = "#003153", radius = .5, label = as.Date(GBif_Marbled$eventDate), group = "GBif Records") %>%
addCircleMarkers(data = Inat_Marbled, lng=Inat_Marbled$longitude, lat=Inat_Marbled$latitude, color = "green", radius = .5, label = as.Date(Inat_Marbled$datetime),group = "INaturalist Records") %>%
addCircleMarkers(lng=APSU_Marbled$DEC_LONG, lat=APSU_Marbled$DEC_LAT, color = "maroon", radius = .5, label = as.Date(APSU_Marbled$VERBATIM_DATE), group = "APSU Records") %>%
addLayersControl(
baseGroups = c("Base Map", "Terrain Map"), overlayGroups = c("APSU Records", "Vertnet Records", "INaturalist Records", "GBif Records"),
options = layersControlOptions(collapsed = FALSE)) %>%
addScaleBar() %>%
addMiniMap(zoomLevelOffset = -4)
APSU_Marbled <- read.csv("https://raw.githubusercontent.com/CJHughes926/Herpmapping_Map_Assignment2/main/APSU_Ambystoma_opacum_TN.csv")
Vertnet_Marbled <- rvertnet::searchbyterm(scientificname = "Ambystoma opacum", limit = 10000)
## Processing request...
##
## Last Query URL: "http://api.vertnet-portal.appspot.com/api/search?q={"q":"scientificname:Ambystoma opacum","l":1000,"c":"False:CvUFCtwDCqwD9wAAAAL_____jIGJmo2LkZqL0o-QjYuek96WkZuah9LNz87M0s_H0s_H_wAA_3RtoKCZi4ygoP8AAP9dno-PmpGYlpGa_wAA_3N0bZaRm5qH_wAA_12biJz_AAD_c3Rtm5CcoJab_wAA_12ekpGX0JeajY-ai5CTkJiG0IqNkdKcnouek5CY0p6SkZfSl5qNj5qLkJOQmIbSntLMyMnLyP8AAP9zf56SkZfQl5qNj5qLkJOQmIbQio2R0pyei56TkJjSnpKRl9KXmo2PmouQk5CYhtKe0szIycvI_wAA__8A_v_-jIGJmo2LkZqL0o-QjYuek96WkZuah9LNz87M0s_H0s_H_wB0baCgmYuMoKD_AF2ej4-akZiWkZr_AHN0bZaRm5qH_wBdm4ic_wBzdG2bkJyglpv_AF2ekpGX0JeajY-ai5CTkJiG0IqNkdKcnouek5CY0p6SkZfSl5qNj5qLkJOQmIbSntLMyMnLyP8Ac3-ekpGX0JeajY-ai5CTkJiG0IqNkdKcnouek5CY0p6SkZfSl5qNj5qLkJOQmIbSntLMyMnLyP8A__4QqEYh214v0Zsk1Mk5AAAAAP3___9IuQNQAFoLCeJaak7PsEpHEANg2YjQhwYSDURvY3VtZW50SW5kZXga4gEoQU5EIChJUyAiY3VzdG9tZXJfbmFtZSIgImFwcGVuZ2luZSIpIChJUyAiZ3JvdXBfbmFtZSIgInN-dmVydG5ldC1wb3J0YWwiKSAoSVMgIm5hbWVzcGFjZSIgImluZGV4LTIwMTMtMDgtMDgiKSAoSVMgImluZGV4X25hbWUiICJkd2MiKSAoQU5EIChRVCAiQW1ieXN0b21hIiAicnRleHRfc2NpZW50aWZpY25hbWUiKSAoT1IgKFFUICJvcGFjdW0iKSAoSVMgIl9fZ2F0b21fXyIgIm9wYWN1bSIpKSkpOhkKDChOIG9yZGVyX2lkKRABGQAAAAAAAPD_SgUIAEDoBw"}"
##
## Matching records: 9456 returned, 9456 available
Vertnet_Marbled <- Vertnet_Marbled$data
Inat_Marbled <- rinat::get_inat_obs(taxon_name = "Ambystoma opacum", maxresults = 10000, quality = "research", geo = TRUE)
GBif_Marbled <- rgbif::occ_data(scientificName = "Ambystoma opacum",
hasCoordinate = TRUE, limit = 10000,
decimalLongitude = "-100, -70",
decimalLatitude = "29, 46.547505", )
GBif_Marbled <- GBif_Marbled$data
APSU_Marbled <- read.csv("https://raw.githubusercontent.com/CJHughes926/Herpmapping_Map_Assignment2/main/APSU_Ambystoma_opacum_TN.csv")
Vertnet_Marbled <- rvertnet::searchbyterm(scientificname = "Ambystoma opacum", limit = 10000)
## Processing request...
##
## Last Query URL: "http://api.vertnet-portal.appspot.com/api/search?q={"q":"scientificname:Ambystoma opacum","l":1000,"c":"False:CvQFCtsDCqwD9wAAAAL_____jIGJmo2LkZqL0o-QjYuek96WkZuah9LNz87M0s_H0s_H_wAA_3RtoKCZi4ygoP8AAP9dno-PmpGYlpGa_wAA_3N0bZaRm5qH_wAA_12biJz_AAD_c3Rtm5CcoJab_wAA_12ekpGX0JeajY-ai5CTkJiG0IqNkdKcnouek5CY0p6SkZfSl5qNj5qLkJOQmIbSntLMyMnLyP8AAP9zf56SkZfQl5qNj5qLkJOQmIbQio2R0pyei56TkJjSnpKRl9KXmo2PmouQk5CYhtKe0szIycvI_wAA__8A_v_-jIGJmo2LkZqL0o-QjYuek96WkZuah9LNz87M0s_H0s_H_wB0baCgmYuMoKD_AF2ej4-akZiWkZr_AHN0bZaRm5qH_wBdm4ic_wBzdG2bkJyglpv_AF2ekpGX0JeajY-ai5CTkJiG0IqNkdKcnouek5CY0p6SkZfSl5qNj5qLkJOQmIbSntLMyMnLyP8Ac3-ekpGX0JeajY-ai5CTkJiG0IqNkdKcnouek5CY0p6SkZfSl5qNj5qLkJOQmIbSntLMyMnLyP8A__4QqEYh214v0Zsk1Mk5AAAAAP3___9IuQNQAFoLCeJaak7PsEpHEANgw9yDEBINRG9jdW1lbnRJbmRleBriAShBTkQgKElTICJjdXN0b21lcl9uYW1lIiAiYXBwZW5naW5lIikgKElTICJncm91cF9uYW1lIiAic352ZXJ0bmV0LXBvcnRhbCIpIChJUyAibmFtZXNwYWNlIiAiaW5kZXgtMjAxMy0wOC0wOCIpIChJUyAiaW5kZXhfbmFtZSIgImR3YyIpIChBTkQgKFFUICJBbWJ5c3RvbWEiICJydGV4dF9zY2llbnRpZmljbmFtZSIpIChPUiAoUVQgIm9wYWN1bSIpIChJUyAiX19nYXRvbV9fIiAib3BhY3VtIikpKSk6GQoMKE4gb3JkZXJfaWQpEAEZAAAAAAAA8P9KBQgAQOgH"}"
##
## Matching records: 9456 returned, 9456 available
Vertnet_Marbled <- Vertnet_Marbled$data
Inat_Marbled <- rinat::get_inat_obs(taxon_name = "Ambystoma opacum", maxresults = 1000, quality = "research", geo = TRUE)
GBif_Marbled <- rgbif::occ_data(scientificName = "Ambystoma opacum",
hasCoordinate = TRUE, limit = 5000,
decimalLongitude = "-90.5, -81.5",
decimalLatitude = "34, 37", )
GBif_Marbled <- GBif_Marbled$data
APSU_Marbled <- as.data.frame(APSU_Marbled)
APSU_Marbled <- subset(APSU_Marbled, is.na(APSU_Marbled$DEC_LAT) == FALSE)
APSU_Marbled$COUNTY <- mgsub(APSU_Marbled$COUNTY, " County", "")
Vertnet_Marbled <- as.data.frame(Vertnet_Marbled)
Vertnet_Marbled <- subset(Vertnet_Marbled, is.na(Vertnet_Marbled$decimallatitude) == FALSE)
Vertnet_Marbled <- subset(Vertnet_Marbled, is.na(Vertnet_Marbled$decimallongitude) == FALSE)
Vertnet_Marbled$county <- mgsub(Vertnet_Marbled$county, " County", "")
Vertnet_Marbled$decimallatitude <- as.numeric(Vertnet_Marbled$decimallatitude)
Vertnet_Marbled$decimallongitude <- as.numeric(Vertnet_Marbled$decimallongitude)
Inat_Marbled <- as.data.frame(Inat_Marbled, )
Inat_Marbled <- subset(Inat_Marbled, Inat_Marbled$coordinates_obscured == "false")
Inat_Marbled <- subset(Inat_Marbled, is.na(Inat_Marbled$latitude) == FALSE)
GBif_Marbled <- as.data.frame(GBif_Marbled)
GBif_Marbled <- subset(GBif_Marbled, is.na(GBif_Marbled$decimalLatitude) == FALSE)
Vertnet_Marbled <- as.data.frame(Vertnet_Marbled)
Vertnet_Marbled <- subset(Vertnet_Marbled, is.na(Vertnet_Marbled$decimallatitude) == FALSE)
Vertnet_Marbled <- subset(Vertnet_Marbled, is.na(Vertnet_Marbled$decimallongitude) == FALSE)
Vertnet_Marbled <- subset(Vertnet_Marbled, Vertnet_Marbled$country == "USA" | Vertnet_Marbled$country == "United States")
Vertnet_Marbled <- subset(Vertnet_Marbled, Vertnet_Marbled$decimallongitude < min(Inat_Marbled$longitude) | Vertnet_Marbled$decimallatitude > max(Inat_Marbled$latitude))
Vertnet_Marbled$county <- mgsub(Vertnet_Marbled$county, " County", "")
Vertnet_Marbled <- subset(Vertnet_Marbled, as.Date(Vertnet_Marbled$eventdate) != "1973-09-30")
Vertnet_Marbled$decimallatitude <- as.numeric(Vertnet_Marbled$decimallatitude)
Vertnet_Marbled$decimallongitude <- as.numeric(Vertnet_Marbled$decimallongitude)
Inat_Marbled <- as.data.frame(Inat_Marbled)
Inat_Marbled <- subset(Inat_Marbled, Inat_Marbled$coordinates_obscured == "false")
Inat_Marbled <- subset(Inat_Marbled, is.na(Inat_Marbled$latitude) == FALSE)
new_df <- APSU_Marbled[,c("DEC_LAT","DEC_LONG")]
new_df2 <- Vertnet_Marbled[,c("decimallatitude", "decimallongitude")]
new_df3 <- Inat_Marbled[,c("latitude","longitude")]
new_df4 <- GBif_Marbled[,c("decimalLatitude","decimalLongitude")]
names(new_df) <- c("x","y")
names(new_df2) <- c("x","y")
names(new_df3) <- c("x","y")
names(new_df4) <- c("x","y")
lot_points <- rbind(new_df, new_df2, new_df3, new_df4)
lot_points <- subset(lot_points, is.na(lot_points$x) == FALSE)
lot_points$x <- as.numeric(lot_points$x)
lot_points$y <- as.numeric(lot_points$y)
lot_points <- subset(lot_points, lot_points$y < 0)
bioclim <- getData(name = "worldclim", res = 2.5, var = "bio", path = "./")
names(bioclim) <- c("Ann Mean Temp","Mean Diurnal Range","Isothermality","Temperature Seasonality",
"Max Temp Warmest Mo","Min Temp Coldest Mo","Ann Temp Range","Mean Temp Wettest Qtr",
"Mean Temp Driest Qtr","Mean Temp Warmest Qtr","Mean Temp Coldest Qtr","Annual Precip",
"Precip Wettest Mo","Precip Driest Mo","Precip Seasonality","Precip Wettest Qtr",
"Precip Driest Qtr","Precip Warmest Qtr","Precip Coldest Qtr")
bio_extent <- extent(x = c(
min(lot_points$y),
max(lot_points$y),
min(lot_points$x),
max(lot_points$x)))
bioclim_extent <- crop(x = bioclim, y = bio_extent)
bioclim_model <- bioclim(x = bioclim_extent, p = cbind(lot_points$y,lot_points$x))
presence_model <- dismo::predict(object = bioclim_model,
x = bioclim_extent,
ext = bio_extent)
gplot(presence_model) +
geom_polygon(data = state, aes(x=long, y = lat, group = group),
fill = "white", color="black") +
geom_raster(aes(fill=value)) +
geom_polygon(data = tn, aes(x=long, y = lat, group = group),
fill = NA, color="black") +
geom_point(data = Inat_Marbled, aes(Inat_Marbled$longitude, Inat_Marbled$latitude), color = "#1f7d1f", size = 2) +
geom_point(data = GBif_Marbled, aes(GBif_Marbled$decimalLongitude, GBif_Marbled$decimalLatitude), color = "dark blue", size = 2) +
geom_point(data = Vertnet_Marbled, aes(Vertnet_Marbled$decimallongitude, Vertnet_Marbled$decimallatitude), color = "dark orange", size = 2) +
geom_point(data = APSU_Marbled, aes(x = APSU_Marbled$DEC_LONG, y = APSU_Marbled$DEC_LAT), color = "maroon", size = 2) +
scale_fill_gradientn(colours=c("brown","yellow","darkgreen"), "Probability") +
coord_fixed(xlim = c(-90.5, -81.5), ylim = c(34.75, 36.75)) +
xlab("Longitude") + ylab("Latitude") + ggtitle("Probability of PILO Occurrence") +
theme_bw() + theme(plot.title = element_text(hjust = 0.5)) + theme(legend.position = "right") +
theme(panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "lightblue"))
## Warning: Use of `Inat_Marbled$longitude` is discouraged. Use `longitude`
## instead.
## Warning: Use of `Inat_Marbled$latitude` is discouraged. Use `latitude` instead.
## Warning: Use of `GBif_Marbled$decimalLongitude` is discouraged. Use
## `decimalLongitude` instead.
## Warning: Use of `GBif_Marbled$decimalLatitude` is discouraged. Use
## `decimalLatitude` instead.
## Warning: Use of `Vertnet_Marbled$decimallongitude` is discouraged. Use
## `decimallongitude` instead.
## Warning: Use of `Vertnet_Marbled$decimallatitude` is discouraged. Use
## `decimallatitude` instead.
## Warning: Use of `APSU_Marbled$DEC_LONG` is discouraged. Use `DEC_LONG` instead.
## Warning: Use of `APSU_Marbled$DEC_LAT` is discouraged. Use `DEC_LAT` instead.
label <- toupper(c(County_Counts$County))
colors <- c("brown","yellow","darkgreen")
leaflet(APSU_Marbled) %>%
addTiles(group = "Base Map") %>%
addWMSTiles("https://basemap.nationalmap.gov/arcgis/services/USGSTopo/MapServer/WmsServer", layers = "0", group = "Terrain Map") %>%
addRasterImage(presence_model, colors = colors, opacity = 0.8) %>%
addPolygons(data= tn_SP, fillColor = "white", color = "black", weight = 1, label = label) %>%
addCircleMarkers(data = Vertnet_Marbled, lng=Vertnet_Marbled$decimallongitude, lat=Vertnet_Marbled$decimallatitude, color = "orange", radius = .5, label = as.Date(Vertnet_Marbled$eventdate), group = "Vertnet Records") %>%
addCircleMarkers(data = GBif_Marbled, lng=GBif_Marbled$decimalLongitude, lat=GBif_Marbled$decimalLatitude, color = "#003153", radius = .5, label = as.Date(GBif_Marbled$eventDate), group = "GBif Records") %>%
addCircleMarkers(data = Inat_Marbled, lng=Inat_Marbled$longitude, lat=Inat_Marbled$latitude, color = "green", radius = .5, label = as.Date(Inat_Marbled$datetime),group = "INaturalist Records") %>%
addCircleMarkers(lng=APSU_Marbled$DEC_LONG, lat=APSU_Marbled$DEC_LAT, color = "maroon", radius = .5, label = as.Date(APSU_Marbled$VERBATIM_DATE), group = "APSU Records") %>%
addLayersControl(
baseGroups = c("Base Map", "Terrain Map"), overlayGroups = c("APSU Records", "Vertnet Records", "INaturalist Records", "GBif Records"),
options = layersControlOptions(collapsed = FALSE)) %>%
addScaleBar() %>%
addMiniMap(zoomLevelOffset = -4)
## Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO", prefer_proj =
## prefer_proj): Discarded ellps WGS 84 in Proj4 definition: +proj=merc +a=6378137
## +b=6378137 +lat_ts=0 +lon_0=0 +x_0=0 +y_0=0 +k=1 +units=m +nadgrids=@null
## +wktext +no_defs +type=crs
## Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO", prefer_proj =
## prefer_proj): Discarded datum World Geodetic System 1984 in Proj4 definition
## Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO", prefer_proj =
## prefer_proj): Discarded ellps WGS 84 in Proj4 definition: +proj=merc +a=6378137
## +b=6378137 +lat_ts=0 +lon_0=0 +x_0=0 +y_0=0 +k=1 +units=m +nadgrids=@null
## +wktext +no_defs +type=crs
## Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO", prefer_proj =
## prefer_proj): Discarded datum World Geodetic System 1984 in Proj4 definition